Abstract
Background and aims: We previously identified DNA methylation differences at multiple CpG loci in a cross-sectional study of individuals with or without diabetic kidney disease (DKD). Here, we aimed to study DNA methylation as a risk factor for the development of kidney failure in individuals with type 1 diabetes and DKD.
Materials and methods: The study included 397 individuals with type 1diabetes and macroalbuminuria at baseline from the Finnish Diabetic Nephropathy (FinnDiane) Study. At baseline, the mean (SD) age was43 (±10.8) years, and 38% were women. Macroalbuminuria (>200 μg/min or >300 mg/24h) was determined from two of three overnight or 24 h urine collections. The study participants were followed up until either kidney failure developed or December 31, 2017. Data on kidney failure requiring dialysis and/or a transplant was collected from the Finnish Care Register for Health Care, study visits, or medical files. Genome-wide blood-derived DNA methylation data was generated for the Infinium HD Methylation EPIC BeadChips (Illumina) in Belfast. After quality control, we extracted M-values (M = log2(β / (1-β)) for 763,064 CpGsites using RnBeads v.2.6.0. M-values for each CpG site were analysed separately with the Cox proportional-hazards model with sex, base lineage, and six estimated white blood cell counts as covariates.
Results: During a median of 7.2 (interquartile range: 2.9-14.0) years of follow-up, 196 individuals developed kidney failure. Eleven CpGs were associated with developing kidney failure with p < 6.6×10-8 - a p-value threshold corrected for the number of studied CpGs. The top CpGcg17944885 is located on chromosome 19 between genes ZNF788P and ZNF625-ZNF20. Higher methylation at this locus was a risk factor for kidney failure (HR [95%CI] = 2.32 [1.95, 2.76], p = 1.4×10-21). Seven significant CpGs were located in or near genes; cg23597162 in JAZF1,cg12272104 in DAZAP1, cg21871803 in AHCYL2, cg12065228 in PQLC2, cg26236214 in ARHGEF7, cg19942083 in the promoter of PTPN6, and cg03262246 <1500 bp from the transcription start site of CDKN2AIPNL. In an independent cohort look-up from Belfast of kidney failure vs controls with no evidence of kidney disease (n = 519), 10 of these CpGs were significantly associated (p < 10-8). Additionally, cg17944885 was strongly associated with DKD in our cross-sectional meta-analysis of the FinnDiane and Belfast cohorts (tot n = 1,304, p =2.0×10-44). In a cohort of 473 individuals with diabetes from the Chronic Renal Insufficiency cohort, six of eleven significant CpGs were associated with eGFR in the whole blood DNA methylation analysis (3.7×10-13 ≤p ≤ 0.05). Furthermore, all six of our eleven top CpGs that were available in the epigenome-wide meta-analysis for eGFR in 33,605 individuals from the Chronic Kidney Disease Genetics Consortium were significantly (p < 1.1×10-7; cg17944885 and CpGs in JAZF1 and PQLC2) or nominally (p < 0.05; CpGs in or near DAZAP1, AHCYL2, and PTPN6) associated with eGFR in their study.
Conclusion: DNA methylation at several CpGs show consistent associations with kidney function and the risk of developing kidney failure.
Materials and methods: The study included 397 individuals with type 1diabetes and macroalbuminuria at baseline from the Finnish Diabetic Nephropathy (FinnDiane) Study. At baseline, the mean (SD) age was43 (±10.8) years, and 38% were women. Macroalbuminuria (>200 μg/min or >300 mg/24h) was determined from two of three overnight or 24 h urine collections. The study participants were followed up until either kidney failure developed or December 31, 2017. Data on kidney failure requiring dialysis and/or a transplant was collected from the Finnish Care Register for Health Care, study visits, or medical files. Genome-wide blood-derived DNA methylation data was generated for the Infinium HD Methylation EPIC BeadChips (Illumina) in Belfast. After quality control, we extracted M-values (M = log2(β / (1-β)) for 763,064 CpGsites using RnBeads v.2.6.0. M-values for each CpG site were analysed separately with the Cox proportional-hazards model with sex, base lineage, and six estimated white blood cell counts as covariates.
Results: During a median of 7.2 (interquartile range: 2.9-14.0) years of follow-up, 196 individuals developed kidney failure. Eleven CpGs were associated with developing kidney failure with p < 6.6×10-8 - a p-value threshold corrected for the number of studied CpGs. The top CpGcg17944885 is located on chromosome 19 between genes ZNF788P and ZNF625-ZNF20. Higher methylation at this locus was a risk factor for kidney failure (HR [95%CI] = 2.32 [1.95, 2.76], p = 1.4×10-21). Seven significant CpGs were located in or near genes; cg23597162 in JAZF1,cg12272104 in DAZAP1, cg21871803 in AHCYL2, cg12065228 in PQLC2, cg26236214 in ARHGEF7, cg19942083 in the promoter of PTPN6, and cg03262246 <1500 bp from the transcription start site of CDKN2AIPNL. In an independent cohort look-up from Belfast of kidney failure vs controls with no evidence of kidney disease (n = 519), 10 of these CpGs were significantly associated (p < 10-8). Additionally, cg17944885 was strongly associated with DKD in our cross-sectional meta-analysis of the FinnDiane and Belfast cohorts (tot n = 1,304, p =2.0×10-44). In a cohort of 473 individuals with diabetes from the Chronic Renal Insufficiency cohort, six of eleven significant CpGs were associated with eGFR in the whole blood DNA methylation analysis (3.7×10-13 ≤p ≤ 0.05). Furthermore, all six of our eleven top CpGs that were available in the epigenome-wide meta-analysis for eGFR in 33,605 individuals from the Chronic Kidney Disease Genetics Consortium were significantly (p < 1.1×10-7; cg17944885 and CpGs in JAZF1 and PQLC2) or nominally (p < 0.05; CpGs in or near DAZAP1, AHCYL2, and PTPN6) associated with eGFR in their study.
Conclusion: DNA methylation at several CpGs show consistent associations with kidney function and the risk of developing kidney failure.
| Original language | English |
|---|---|
| Article number | 38 |
| Pages (from-to) | S21 |
| Number of pages | 1 |
| Journal | Diabetologia |
| Volume | 65 |
| Issue number | Supplement 1 |
| Publication status | Published - 30 Oct 2022 |
| Event | 58th Annual Meeting of the European Association for the Study of Diabetes - Stockholm, Sweden Duration: 19 Sep 2022 → 23 Sep 2022 https://www.easd.org/annual-meeting/easd-2022.html |
